title: 0.01uM_Paraquat_A549, A_201

description:
A_201
A549_Paraquat_0.01uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0.01uM Paraquat


title: Hepatocyte organoids, RGF +T3 +DEX, Day 3, 1

status: Public on May 15 2024

type: SRA

city: Boston

first: Yuchen

last: Liu

state: Massachusetts

address: 188 Longwood Avenue, REB 514B

country: USA

institute: Harvard school of dental medicine

library_source: transcriptomic

data_processing:
Sequence alignment were performed using STAR aligner.
Paired reads were then counted using ‘featureCounts’ in The Subread software
Raw counts were normalized using the edgeR package
Assembly: mm10
Supplementary files format and content: tab delimited text file include normalized CPM values for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: liver

growth_protocol: The HOs were maintained in the original HO growth medium with growth factors (GFs) (+GF medium). The +GF medium for  HO culture contains Advanced DMEM/F12 with B27 minus vitamin A, 10mM HEPES, GlutaMAX™, and Penicillin-Streptomycin (Thermo Fisher Scientific), 15% RSPO1 conditioned medium (home-made), 3μm CHIR99021 (MCE), 50ng/ml EGF (Biolegend), 25ng/ml HGF (Biolegend), 50ng/ml FGF7 (Peprotech), 50ng/ml FGF10 (Biolegend), 1μM A83-01 (Sigma), 5μM Rho Inhibitor γ-27632 (MCE), 10nM gastrin (Sigma), 10 mM Nicotinamide (Sigma), and 1mM N-acetylcysteine (Sigma).

extract_protocol:
Organoids were retrieved from BME using Cultrex Organoid Harvesting Solution and pelleted by centrifuge at 50g for 3 minutes. RNA was isolated from the organoid pellet using PureLinkTM RNA mini kit (Thermo fisher scientific) according to the manufacturer's instruction.
DNA was removed from RNA using RapidOut DNA Removal Kit (Thermo Fisher Scientific) according to the manufacturer's instruction. After measuring RNA quantity and quality by Agilent 2200 TapeStation, 400ng-1000ng RNA per sample reaction were used for mRNA isolation using NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). Libraries were prepared using xGen™ RNA Library Prep Kit (IDT) according to the manufacturer's instruction.

treatment_protocol: The HOs were switched to the maturation medium for HO maturation. The basal medium for human and mouse HO maturation is Growth factors removed (RGF) medium, which includes William's E Medium with B27 minus vitamin A, 10mM HEPES, GlutaMAXTM and Penicillin-Streptomycin (Thermo Fischer Scientific), 50μg/ml Primocin (InvivoGen), 15% RSPO1 conditioned medium (house-made), 3μM CHIR99021 (MCE), 1μM A83-01 (MCE), 5μM Rho Inhibitor γ-27632 (MCE), 10nM gastrin (Sigma), 2.5 mM Nicotinamide (Sigma), and 1.25 mM N-acetylcysteine (Sigma). Additional components were added to RGF medium for hepatic maturation of HOs. For maturation of mouse HOs, these medium incude: RGF +T3: 10nM Triiodothyronine(T3) in RGF medium; RGF +DEX: 200nM dexamethasone (DEX) in RGF medium; RGF +T3 +DEX: 10nM T3 and 200nM DEX in RGF medium. For HO dedifferentiation, the HOs were cultured in the RGF +T3 condition for 6 days, and switched to +GF condition for another 6 days. To overexpress CTNNB1ΔN90 in the HOs, AAV-TBG-CTNNB1ΔN90 was mixed with fragmented HOs in BME at a concentration of 2x10^10 GC/ml during passage.

tag: tissue

value: liver

tag: cell line

value: Hepatocyte organoids

tag: cell type

value: hepatocytes

tag: genotype

value: wild type

tag: treatment

value: RGF +T3 + DEX, Day3

tag: time


title: group2,Vehicle2_2

city: xinxing

first: huijie

last: yang

address: Hongqi District, Xinxiang City

country: China

institute: Xinxiang Medical University

data_processing:
Using BGISEQ-500 sequencing platform
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.

molecule: total RNA

organism: Homo sapiens

source_name: Liver cancer

growth_protocol: organoids were maintained  in humidified atmosphere with 5% CO2 at 37°C with bioGenousTM Hepatocellular Carcinoma Organoid Kit Catalog: K2105-HCC

extract_protocol:
Lysis of organoids with Trizol regent and harvesting of RNA.
RNA libraries for RNA-seq were prepared using BGISEQ-500 protocols.

treatment_protocol: First, three different of human organoid samples were constructed, and then each group of samples was treated with Vehicle and 10 μM Atosiban

value: Liver cancer

value: organoid

value: human organoids

tag: group


title: 0uM_Paraquat_A549, A_206

city: Durham

first: Rasim

last: Barutcu

state: NC

address: 6 Davis Drive

institute: ScitoVation

description:
A_206
A549_Paraquat_0uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

data_processing:
Reads were mapped to the Ensembl human reference genome (hg38) using HISAT2 (version 2.05) (Zhang et al. 2021).
Alternative splicing analysis of RNA-Seq data was performed with vast-tools version 2 (Tapial et al. 2017). The INCLUSION files xontain information about the quality and raw percent spliced-in (PSI) values of each replicate. The headers of the INCLUSION files contain the cell type, the chemical, the dose, and the replicate number separated by underscores '_'. More information about this file type ccan be found at: https://github.com/vastgroup/vast-tools
Assembly: hg38
Supplementary files format and content: Read count table
Supplementary files format and content: Metadata table
Supplementary files format and content: Splicing inclusion files showing the raw percent spliced-in (PSI) values

growth_protocol: A549 cells were obtained from the American Type Culture Collection (ATCC). Proliferation media consisted of Dulbecco’s Modified Essential Medium (Gibco) with 10% FBS (Atlanta Biologicals) and 1% penicillin-streptomycin (Gibco). The plating medium consisted of Dulbecco’s Modified Essential Medium (Gibco) with 10% Heat-Inactivated FBS (HI FBS; Atlanta Biologicals) and 1% penicillin-streptomycin (Gibco). For passaging, cells were washed with sterile DPBS and enzymatically removed using 0.25% trypsin-EDTA (Gibco). In preparation for the proliferation assay, A549 cells were thawed (2.0 x 106, passage 3) and placed into a T25 flask (CytoOne; USA Scientific, Ocala, FL). After 5 days in culture, cells were passaged into a T75 flask (2.0 x 106, passage 4) using a plating medium (10% HI FBS). After 5 days, cells were plated at a density of 35,000 cells/well in black-walled, clear-bottom, tissue-culture-treated 96-well plates (Greiner Bio-One) using a plating medium (10% HI FBS). Cells were cultured for 48 h in 96-well plates prior to treatment.

extract_protocol:
Nextera XT DNA Library Preparation Kit
polyA enrichment
Illumina 150bp paired-end reads

value: lung adenocarcinoma cell line

value: A549 cells treated with 0uM Paraquat


title: group2,Vehicle2_1


title: Hepatocyte organoids, RGF +T3, Day 3, 3

value: RGF +T3, Day3


title: p4_2

city: Beijing

first: Longxiang

last: Su

state: Beijing

address: 1 Shuaifu Yuan

department: Department of Critical Care Medicine

institute: Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Science

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Comparison, filtering, barcode counting, and unique molecular identifier (UMI) counting were performed using Cell Ranger software to create a feature-barcode matrix (https://support.10xgenomics.com/single-cell-gene-expression/software /download/ latest). To eliminate cells with poor sequencing quality, we established specific criteria for each cell, including UMI counts between 1,000 and 20,000, gene counts greater than 500, and mitochondrial gene percentages less than 5%. After filtering, we loaded the resulting gene-barcode matrix into Seurat v4 and performed subsequent analysis.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: bronchoalveolar lavage fluid (BALF)

extract_protocol:
Collection of bronchoalveolar lavage fluid (BALF) followed the recommended bronchoscopy procedure. After the patient was anesthetized and received analgesia, 0.9% saline was injected into the middle lobe of the right lung or the upper lobe of the left lung to obtain BALF in a volume of 30 mL. Freshly collected BALF was passed through a 70 μm nylon cell filter (ThermoFisher Scientific, 22-363-548) to remove clots and debris. The supernatant was then poured off by centrifugation at 300 g for 5 min at 4°C (LICHEN, LC-LX-LR55C). Cells were resuspended in PBS (Bioss, C7033) containing 0.04% BSA (Solarbio, s9020) and counted using a Countstar Rigel S2 instrument (Shanghai Ruiyu Biotechnology). We adjusted the concentration of the cell suspension to 300-600 live cells per microliter.
Single cell capture and downstream library construction was performed using the Chromium Next GEM Single Cell 3' GEM Kit v3.1 (10x Genomics), following the manufacturer's protocol. Briefly, single cell gel bead emulsion (GEM) was generated by loading a total volume of 70 μL of Master Mix and cell suspension (containing 6000 cells), a volume of 50 μL of barcoded gel beads, and a volume of 45 μL of separator oil onto a Chromium Chip K. The GEM was then loaded onto a Chromium Chip K with a total volume of 70 μL of barcoded beads and a volume of 45 μL of separator oil. The gel beads were dissolved and primers released immediately after GEM generation. Polyadenylated mRNA was reverse-transcribed into cDNA. full-length cDNA was PCR-amplified with cellular barcode identifiers to prepare and standardize sequencing libraries. Finally, the libraries were sequenced using an Illumina Novaseq 6000 sequencer with a sequencing depth of at least 100,000 reads per cell using a paired-end 150 bp (PE150) read strategy (Bestopcell, Beijing).

value: bronchoalveolar lavage fluid (BALF)

value: after treatment in ICU and with MS change value ≥1 point (t2)


title: group1,Atosiban1_1


title: Brain Control_3

city: Irvine

first: Saurabh

last: Chatterjee

state: California

address: 5270 California Avenue

department: Department of Environmental and Occupational Health

institute: University of California, Irvine

data_processing:
The quality of the sequencing was first assessed using the fastQC tool (v0.11.9) on the paired end reads. Raw reads were then illumina adapter and quality trimmed and filtered by a length of 20 bases using trimmomatic (v0.39). Trimmed reads were aligned to indexed mouse reference genome mm10 using short read aligner hisat2 (v2.2.1) and gene expression levels were quantified using featureCount from Subread (v2.0.1) for all annotated genes and samples. Differential gene expression analysis was done using R package DESeq2(v1.22.2) implementing a negative binomial model of the gene count with an FDR (false discovery rate) cut-off of 0.05. PCA plots and heatmaps were generated using DESeq2(v1.22.2).
Assembly: Trimmed reads were aligned to indexed mouse reference genome mm10 using short read aligner hisat2 (v2.2.1) and gene expression levels were quantified using featureCount from Subread (v2.0.1) for all annotated genes and samples
Supplementary files format and content: Differential Gene Expression Table obtained from analysis, comparing the log2 fold changes in Control vs Heat Stress groups. Differential gene expression analysis was done using R package DESeq2(v1.22.2) implementing a negative binomial model of the gene count with an FDR (false discovery rate) cut-off of 0.05.
Supplementary files format and content: Processed data is in microsoft excel file format converted from CSV.

molecule: cytoplasmic RNA

source_name: Brain

extract_protocol:
Samples of frozen tissue were cut and weighed to obtain  25mg. The tissue was placed into a 1.7mL microfuge tube with 500uL Trizol (Life Technologies) and kept on ice. The tissue was homogenized with a disperser (IKA) with three cycles of 20 seconds of dispersing (speed 6- liver; speed 3- brain) followed by 10 seconds of rest. The tube was kept in an ice water bath during the homogenization. After the homogenization, the tube was centrifuged for 12,000 x g for 1 minute. The supernatant was removed to a new 1.7mL microfuge tube without disturbing cell debris that may have been pelleted. The remainder of the protocol followed the instructions for the Zymo Research Direct-zol RNA miniprep kit with some minor edits. An equal volume of ethanol (90-100%) was added to the supernatant and briefly vortexed. The mixture was transferred to the Zymo Spin IICR column in a collection tube and centrifuged for 30 seconds at 12,000 x g. The flow-through was discarded and 400uL of Direct-zol RNA Wash Buffer was added to the column. The column was centrifuged for 30 seconds at 12,000 x g. A mixture of DNase digestion buffer (75uL) and DNase I (5uL) was added to the column and incubated at room temperature for 15 minutes. After the DNase I incubation, 400uL of Direct-zol RNA PreWash was added to the column, followed by centrifugation for 30 seconds at 12,000 x g. The flow-through was discarded and the PreWash step was repeated. The flow through was discarded and 700uL of Direct-zol RNA Wash Buffer was added to the column and centrifuged for 2 minutes at 12,000 x g. The spin column was removed to a fresh collection tube and centrifuged again for 1 minute at 12,000 x g. To elute the RNA, 30uL of DNase/RNase-free water was added directly to the column and incubated for 5 minutes at room temperature. The RNA was eluted by centrifugation for 1 min at 16,000 x g into a new 1.7mL lo-bind RNase-free microtube. The RNA was stored at -80oC.
Library construction is performed according to the Illumina TruSeq mRNA stranded protocol. The input quantity for total RNA will be ~ 550ng and mRNA will be enriched using oligo dT magnetic beads. The enriched mRNA is chemically fragmented for three minutes. First-strand synthesis uses random primers and reverse transcriptase to make cDNA. After second-strand synthesis, the ds cDNA is cleaned using AMPure XP beads, and the cDNA is end-repaired and then the 3’ ends are adenylated. Illumina unique dual indexed adapters are ligated on the ends and the adapter ligated fragments are enriched by nine cycles of PCR. The resulting libraries will be validated by qPCR and sized by Agilent Bioanalyzer DNA high-sensitivity chip.
The concentrations for the libraries will be normalized and multiplexed together. The multiplexed libraries will be sequenced using paired-end 100 cycles chemistry on the NovaSeq 6000. We will target 20M reads per sample.

treatment_protocol: To study the underlying pathological changes in exposure to heat stress, an aging mouse model was used. Aged C57BL6/J (24 months old) mice were exposed to heat stress at 40± 0.5°C with a relative humidity of 60% ± 5% for three hours/day for 15 days mimicking a periodic heat wave exposure.

value: Brain

value: Control

value: WT


title: p4_1

description: 10x Genomics

value: when admission to the ICU (t1)


title: Hepatocyte organoids, RGF +T3, Day 3, 2

value: liver


title: Hepatocyte organoids, RGF +T3 +DEX, Day 3, 3

value: Hepatocyte organoids


title: Brain Control_2


title: group3,Vehicle3_1


title: p3_2

description: 10x Genomics


title: Hepatocyte organoids, RGF +T3, Day 3, 1

value: hepatocytes


title: Brain Control_1


title: Hepatocyte organoids, +GF, 3

value: wild type


title: group1,Vehicle1_3


title: group1,Vehicle1_2


title: APRIL-BB-1XX_IL-18_HTO

city: Duarte

first: Anastasia

middle: I

last: Kousa

state: CA

address: 1500 E Duarte Rd

department: Hematology / HCT

institute: City of Hope

description:
20230508_MM_IL-18_singlecell.h5ad
T_cells.h5ad
Mac_mono.h5ad

library_source: other

data_processing:
FASTQ files were processed using the 10x Cell Ranger package (v6.1.2). The Cell Ranger generated filtered_feature_bc_matrix.h5 files were processed using the pipeline available on the shunPykeR4 GitHub repository which implements Python and R code for streamlined analysis with Scanpy5 and other python implemented tools. Genes that were not expressed in any cell, in addition to ribosomal and hemoglobin genes, were removed prior to downstream analysis. Each cell was then normalized to a total library size of 10,000 reads and gene counts were log- transformed using the log(X+1) formula, in which log denotes the natural logarithm. Principal component analysis was applied to reduce noise prior to data clustering. To select the optimal number of principal components to retain for each dataset, the knee point (eigenvalues smaller radius of curvature) was used. Leiden clustering6 was used to identify clusters within the PCA- reduced data.
Quality of the single cells was computationally assessed based on total counts, number of genes, mitochondrial and ribosomal fraction per cell, with low total counts, low number of genes (≤1000) and high mitochondrial content (≥0.2) as negative indicators of cell quality. Cells characterized by more than one negative indicator were considered as “bad” quality cells. To remove bad quality cells and contaminants in an unbiased way, we assessed them in a cluster basis rather than individually. Leiden clusters with a “bad” quality profile and/or a high number of contaminating cells were removed. Scrublet7 was used to filter out doublets.
For CITE-seq, filtered_feature_bc_matrix.h5 files were again loaded and concatenated in the same fashion as RNA files. Total raw counts were obtained for each epitope/antibody read, and data were plotted on the UMAP projection that was generated with scRNAseq data. Dotplot were generated using transformed and normalized expression.
Patient data for myeloma-associated antigen expression was obtained from the Nature Communications publication by Tirier et al. (2021) and accessed on GEO (GSE161801). Sequencing samples denoted as “CD138+ tumor” were taken and concatenated with Scanpy. Upon clustering data with Leiden and by patient ID, we removed clusters that were not homogenously categorized as a single patient or did not have expression of the markers SDC1, SLAMF7, CD38 (described method by Tirier et al.)12. RNA expression for genes of interest was imputed with MAGIC13 and then plotted as UMAP projection of heatmap.
Assembly: mm10-20-a
Supplementary files format and content: 20230508_MM_IL-18_singlecell.h5ad: H5AD file with raw and normalized read counts and cell annotation for all cells (after bad quality cell filtering)
Supplementary files format and content: T_cells.h5ad: H5AD file with raw and normalized read counts and cell annotation of T-cells only (after bad quality cell filtering)
Supplementary files format and content: Mac_mono.h5ad: H5AD file with raw and normalized read counts and cell annotation of macrophages/monocytes only (after bad quality cell filtering)
Supplementary files format and content: adata_Tirier_Nat_comm_2021_filtered.h5ad: H5AD of reanalyzed data from GEO accession #GSE161801 after MAGIC imputation
Supplementary files format and content: adata_Tirier_Nat_comm_2021_filtered_magic.h5ad: H5AD of reanalyzed data from GEO accession #GSE161802
Supplementary files format and content: filtered_feature_bc_matrix files (barcodes, features, matrix): contain only detected cell-associated barcodes in MEX format; each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column)
Supplementary files format and content: filtered_feature_bc_matrix.h5: same information as filtered_feature_bc_matrix in HDF5 format
Supplementary files format and content: raw_feature_bc_matrix files (barcodes, features, matrix): contain all detected barcodes in MEX format; each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column)
Supplementary files format and content: raw_feature_bc_matrix.h5: same information as raw_feature_bc_matrix in HDF5 format
Library strategy: CITE-seq

molecule: other

source_name: bone marrow

extract_protocol:
CAR T-cell treated mice were harvested for bone marrow on day 7 of experiment (4 days after CAR T-cells). Cells were erythrocyte-lysed and stained with Fc-block. Cells were then labeled with fluorescent antibodies and DAPI for FACS sorting and hashtag oligonucleotide (HTO) antibodies (Biolegend) to barcode each mouse for identification post-sequencing. Cells were FACS-sorted for CD45+/CD3+ T-cells and CD45+/CD3- non-T-cells. Cells were re-pooled at 1:2 T- cells:non-T-cells and stained with FcX (Biolegend) followed by Biolegend TotalSeqA mouse universal cocktail (for CITE-seq). ~100,000 cells from each biological group were submitted for single-cell sequencing (n=3 mice per group, ~30,000 cells /mouse).
Single-cell RNA sequencing of FACS-sorted cell suspensions was performed on the Chromium instrument (10X genomics) following the user guide manual for 3′ v3.1. In brief, FACS- sorted cells were washed once with PBS containing 1% bovine serum albumin (BSA) and resuspended in PBS containing 1% BSA to a final concentration of 1,700–2,000 cells per μl. The viability of cells was above 80%, as confirmed with 0.2% (w/v) Trypan Blue staining (Countess II). Cells were captured indroplets. Following reverse transcription and cell barcoding in droplets, emulsions were broken, and cDNA was purified using Dynabeads MyOne SILANE followed by PCR amplification as per manual instruction. About 30,000 cells were targeted for each sample. Samples were multiplexed together on one lane of 10x Chromium (using HTO) and specific extracellular protein epitope characterized (using Antibody Derived Tag, Biolegend TotalSeqA) following a previously published protocol3. Final libraries were sequenced on Illumina NovaSeq S4 platform (R1 – 28 cycles, i7 – 8 cycles, R2 – 90 cycles) at a depth of ~575 million reads per sample. HTO and CITE were sequenced at ~88 million reads per sample.

treatment_protocol: Myeloma bearing mice were injected with 4E5 MOPC315.BM (TACI KO) on day 0, followed by 2E6 APRIL-BB-1XX or APRIL-BB-1XX/IL-18 T-cells on day 3.

value: bone marrow

value: CD45+ bone marrow

value: BALB/c

value: APRIL-BB-1XX_IL-18 CAR T-cells


title: p3_1

description: 10x Genomics


title: group1,Vehicle1_1

value: Liver cancer

value: organoid

value: human organoids


title: p2_2

description: 10x Genomics

value: bronchoalveolar lavage fluid (BALF)


title: MV4;11_DOX_2

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
The quality of paired reads were checked using FASTQC (v0.11.7)
Reads were aligned against human mm10 genome using HISAT2 (v2.0.5)
Each gene-level raw counts were calculated using featureCounts (v1.5.2)
Assembly: hg38
Supplementary files format and content: The CSV files include raw read counts for each sample

growth_protocol: The cells were cultured in RPMI1640 medium with 10% fetal bovine serum FBS and 1% penicillin and streptomycin.

extract_protocol:
RNA was extracted using Quick-RNA MiniPrep (Zymo) following manufacturer's protocol
RNA libraries were prepared according to the Illumina protocol (Nextera817 XT DNA Sample Preparation Kit).

treatment_protocol: To induce knockdown of TRAF6, the cells were cultured with doxycycline (1μg/mL) for 7 days.

value: leukemic cells

value: TRAF6 knockdown

value: Doxycycline


title: p2_1

description: 10x Genomics


title: APRIL-BB-1XX_IL-18_CITE

molecule: protein


title: MV4;11_DOX_1


title: Hepatocyte organoids, +GF, 1

value: Control


title: APRIL-BB-1XX_IL-18_GEX


title: p1_2

description: 10x Genomics

value: after treatment in ICU and with MS change value ≥1 point (t2)


title: APRIL-BB-1XX_HTO

value: APRIL-BB-1XX CAR T-cells


title: 27S NaHCO3

city: El Paso

first: Eda

last: Kocui

state: TX

address: 500 W. University Avenue

department: Chemistry and Biochemistry

institute: University of Texas at El Paso

description: 23S ribosomal RNA

data_processing:
Base calls were performed uising Illumina RTA version 1.18. 54
The next generation sequencing reads were aligned to the rrlB and rrsB  genes of Bl21 (DE3)  E Coli and the mutations were counted using Shape-Mapper 1.2

organism: Escherichia coli

source_name: Escherichia Coli cells

growth_protocol: The cells were grown at 37ºC in 200 mL of media containing 10g/L tryptone, 1g/L yeast extract, 100μg/mL carbenicillin, and 34μg/mL chloramphenicol. When the cell reached an optical density at 600 nm of about 0.3, the cell growth was arrested by adding 200 ml of ice.

extract_protocol:
The ribosomal particles were isoalate using a  20-40% gradients were made in a buffer consisting of 20mM HEPES KOH pH 7.5, 150mM NH4Cl, 1mM MgCl2 and 4mM BME.
The NGS sequencing library was performed following the randomer workflow of the Selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling(SHAPE-MaP) protocol(Smola et al. 2015)

treatment_protocol: the 27S ribosomal particles were treated with CMCT and NaHCO3 , NaHCO3 alone.

tag: strain

value: BLR (DE3) dDbpA, expressin R331A DbpA

value: Escherichia Coli cells


title: p1_1

description: 10x Genomics

value: when admission to the ICU (t1)


title: 27S CMCT and NaHCO3 replicated 2

description: 23S ribosomal RNA

value: CMCT and NaHCO3


title: APRIL-BB-1XX_CITE

value: bone marrow

value: CD45+ bone marrow


title: covid_p4_2

description: 10x Genomics


title: MV4;11_untreated_1

value: Untreated


title: 27S CMCT and NaHCO3 replicated 1

description: 23S ribosomal RNA


title: HEL_DOX_2

source_name: HEL

value: HEL


title: covid_p4_1

description: 10x Genomics


title: Two pooled e14.5 pituitary glands from C57BL6 strain

city: Ann Arbor

first: Lev

last: Prasov

state: MI

address: 1241 Catherine Street, 5704 Med Sci II

department: Department of Human Genetics

institute: University of Michigan

data_processing:
Samples were demultiplexed with Cellranger Single Cell Software Suite 3.0.3-3.1.0
Cellranger outputs were analyzed in R using the ‘Seurat’ 3.1.2 package (Butler et al. 2018; Stuart et al. 2019).
Core Seurat functions were used to read in cellranger output files, integrate samples, generate uniform manifold approximation and projection (UMAP) plots, calculate clusters, perform differential gene expression analyses, and generate plots of expression data.
Assembly: fastq files for the e12 were aligned to a modified University of California Santa Cruz mm10 (GRCm38) reference genome containing an additional artiificial gene for YFP. Fastq files for the e14 sample were aligned to a modified University of California Santa Cruz mm10 (GRCm38) reference genome containing amended annotation for the Prop1 3’ untranslated region (Cheung et al. 2018b)
Supplementary files format and content: zipped versions of the matrix tables, with list of barcodes (column names for matrix) and features (i.e. genes, row names for matrix)

source_name: pituitary gland

extract_protocol:
One e12.5 pituitary gland from a retinoic acid reporter mouse (RARE-LacZ JAX strain #008477) was dissociated in an enzyme mix containing 0.5% w/v collagenase type 2 (Lorne Laboratories, Reading, UK), 0.1× trypsin (Invitrogen, Carlsbad, CA), 50 μg/mL DNase I (Worthington Biochemical, Lakewood, NJ), and 2.5 μg/mL amphotericin B (Fungizone; Invitrogen) in Hanks balanced salt solution (Invitrogen) for 1 hour at 37°C.  For the e14.5, 2 C57BL/6J e14.5 samples were dissociated into single cells in 50 μl of a solution containing 1mg/ml Papain (Roche, cat#10108014001), 5mM L-Cysteine, 1mM EDTA, and 0.6mM 2-mercaptoethanol. Dissociation was performed at 37°C for 5 minutes, with titration every 2 minutes.
Single-cell RNA libraries were prepared by the University of Michigan’s Advanced Genomics Core under a standardized pipeline on the 10x Genomics Chromium platform and controller, following manufacturer’s instructions for Single Cell 3’ v3 reagents, and sequenced on the NovaSeq6000 platform with an S4 chip.  From our previous description in Cheung et al., 2018 Endocrinology: Following generation of single-cell gel bead-in-emulsions (GEMs), reverse transcription was performed and the resulting post-GEM reverse transcription product was cleaned up using DynaBeads MyOne silane beads (Thermo Fisher Scientific, Waltham, MA). The cDNA was amplified, SPRIselect (Beckman Coulter, Brea, CA) cleaned and quantified, and then enzymatically fragmented and size selected using SPRIselect beads to optimize the cDNA amplicon size prior to library construction. An additional round of double-sided SPRI bead cleanup was performed after end repair and A-tailing. Another single-sided cleanup was done after adapter ligation. Indexes were added during PCR amplification and a final double-sided SPRI cleanup was performed. Libraries were quantified by KAPA quantitative PCR for Illumina adapters (Roche, Pleasanton, CA) and size was determined by Agilent TapeStation D1000 tapes. Read 1 primer sequences were added to the molecules during GEM incubation. P5, P7, and sample index and read 2 primer sequences were added during library construction via end repair, A-tailing, adaptor ligation, and PCR. Libraries were generated with unique sample indices for each sample.

value: pituitary gland

value: total pituitary cells

tag: age

value: wild type


title: covid_p3_2

description: 10x Genomics

value: bronchoalveolar lavage fluid (BALF)


title: Hepatocyte organoids, +GF, 2

value: liver

value: Hepatocyte organoids

value: hepatocytes


title: APRIL-BB-1XX_GEX

value: BALB/c


title: e12.5 pituitary gland from a retinoic acid reporter mouse (RARE-LacZ JAX strain #008477)

value: RARE-LacZ


title: HEL_untreated_1

value: leukemic cells

value: Control


title: HEL_DOX_1

value: TRAF6 knockdown

value: Doxycycline


title: RPMA ONB tumor rep3

first: Trudy

last: Oliver

email: tgo@duke.edu, trudy.oliver@duke.edu

address: Duke University, Box 3813, LSRC Room C138B, 308 Research Drive

department: Pharmacology & Cancer Biology

institute: Duke University

description: 10X Genomic 3' GEX

data_processing:
Demulitplexed with 10x cellranger mkfastq to create fastq files with sample index (I1, I2) and read files (R1, R2).
Reads were aligned to the mouse genome (refdata-cellranger-mm10) from 10X Genomics and count barcodes and UMIs were generated using cellranger count v7.1.0 .
Downstream visualization and further analysis of scRNA seq data was performed in R with Seurat and/or Python with Scanpy.
Assembly: mm10-2020-A
Supplementary files format and content: Filtered feature-barcode matrices  from cellranger count.

source_name: tumor cells

extract_protocol:
Each tumor sample was subject to enzymatic/mechanical digestion into a single cell suspension. 10x Genomics gel beads and reverse transcription reagents were added to cell suspensions and loaded to a chromium single cell controller to form gel-bead-in emulsions (GEMs). From GEMs, cDNA was generated from barcoded mRNA and subsequent A tailing, end repair, adaptor ligation, and sample indexing was performed according to manufacturer. Libraries were assessed on Agilent D5000 ScreenTape on an Agilent Tech 2200 tapestation system and quantified by Kapa Biosystems Library Quantification Kit for Illumina Platforms. Libraries were sequenced on the Novaseq 6000 w 2x150 paired end seq targeting ~30k reads/cell.
10X Genomics Single-Cell 3' RNA Dual Index v3

value: tumor cells

value: Rb1 fl/fl; Trp53 fl/fl; H11b-LSL-MycT58A-Ires-Luc; Ascl1 fl/fl (RPMA)


title: UOK120 cells - second input

city: Nanjing

first: Yi

last: Chen

address: 22 Hankou Road

department: Medical school

institute: Nanjing Unversity

description: UOK120 input

library_source: genomic

data_processing:
ChIP-seq data were obtained using an Illumina Hiseq 2000 sequencerand sequencing reads were de-multiplexed by Illumina pipeline.
ChIP-seq data were mapped to the human genome (hg19) using Bowtie algorithm with up to 2 mismatch allowed and reads mapping to more than 20 locations along the genome were discard.
ChIP-seq data generated form IgG were used against the sample data in calling enriched regions and to control for false discovery rate (FDR).
Peaks were called using MACS version 2, with q-value to 0.05.
Assembly: hg19

molecule: genomic DNA

source_name: renal carcinoma

growth_protocol: Cells were cultured in DMEM supplemented with 10% FBS (Gibco) and 1% penicillin/streptomycin.

extract_protocol:
Cells were cultured and subsequently crosslinked in 1% formaldehyde and processed according to the protocol from the Pierce™ Agarose ChIP Kit. ChIP was performed in UOK109and UOK120 cells using the TFE3 antibody. Immunoprecipitated genomic DNA was used for sequencing analysis.
The purified DNA fragments were end-repaired, tail-added and joined to construct sequenced libraries.

value: renal carcinoma

value: UOK120 cell line


title: RPMA ONB tumor rep2

description: 10X Genomic 3' GEX


title: UOK120 cells - second TFE3 chip

description: UOK120 CHIP

value: TFE3 antibody


title: UOK109 cells TFE3 chip

description: UOK109 CHIP

value: UOK109 cell line


title: HEL_untreated_2

value: HEL

value: Untreated


title: covid_p2_2

description: 10x Genomics

value: bronchoalveolar lavage fluid (BALF)

value: after treatment in ICU and with MS change value ≥1 point (t2)


title: covid_p3_1

description: 10x Genomics

value: when admission to the ICU (t1)


title: MV4;11_untreated_2


title: ISOGK treated 4

city: Hefei City

first: ZHIDAN

last: ZHANG

state: Anhui Province

address: No. 96 Jinzhai Road

institute: University of Science and Technology of China

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Liver

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qisagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Liver

value: Apoe-/-

value: ISOGK


title: UOK109 cells input

description: UOK109 iput


title: Brain Heat Stress_1

value: Brain

value: Heat Stress

value: WT


title: RPMA ONB tumor rep1

description: 10X Genomic 3' GEX

value: tumor cells


title: covid_p1_2

description: 10x Genomics


title: covid_p2_1

description: 10x Genomics


title: ISOGK treated 3


title: Normal_5

city: KunMing

first: Ping

last: Yuan

state: YunNan

address: No.295 Xichang Road, Wuhua District

institute: The First Affiliated Hospital of Kunming Medical University

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Supplementary files format and content: excel,expression profile

source_name: Blood plasma

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

value: Blood plasma

value: healthy control

value: Isolation and purification from human plasma

tag: molecule subtype

value: Small RNA


title: Normal_4


title: RPM ONB tumor rep1

description: 10X Genomic 3' GEX

value: Rb1 fl/fl; Trp53 fl/fl; H11b-LSL-MycT58A-Ires-Luc (RPM)-Rosa26-LSL-Cas9-Ires-Gfp  (RPM-GFP)


title: Normal_3


title: RPMA GBC Allograft rep1

description: 10X Genomic 3' GEX

data_processing:
Demulitplexed with 10x cellranger mkfastq to create fastq files with sample index (I1, I2) and read files (R1, R2).
Reads were aligned to the custom mouse genome (refdata-cellranger-mm10) from 10X Genomics plus GFP.CDS and CellTag.UTR sequences (as described in Kong et al., Nature Protocols, 2020) using cellranger mkref. Count barcodes and UMIs were then generated using cellranger count v7.1.0 .
Downstream visualization and further analysis of scRNA seq data was performed in R with Seurat and/or Python with Scanpy.
Assembly: Custom mm10-2020-A plus GFP.CDS and CellTag.UTR sequences.
Supplementary files format and content: Filtered feature-barcode matrices from cellranger count.

source_name: allograft tumor

extract_protocol:
Organoids were subject to dissociation by TrypLE for 30 minutes into a single cell suspension. Allograft tumor  was subject to enzymatic/mechanical digestion into a single cell suspension. 10x Genomics gel beads and reverse transcription reagents were added to cell suspensions and loaded to a chromium single cell controller to form gel-bead-in emulsions (GEMs). From GEMs, cDNA was generated from barcoded mRNA and subsequent A tailing, end repair, adaptor ligation, and sample indexing was performed according to manufacturer. Libraries were assessed on Agilent D5000 ScreenTape on an Agilent Tech 2200 tapestation system and quantified by Kapa Biosystems Library Quantification Kit for Illumina Platforms. Libraries were sequenced on the Novaseq 6000 w 2x150 paired end seq targeting ~50-70k reads/cell.
10X Genomics Single-Cell 3' RNA Dual Index v3

value: allograft tumor

value: tumor

value: Rb1 fl/fl; Trp53 fl/fl;H11b-LSL-MycT58A-Ires-Luc; Ascl1 fl/fl (RPMA)

value: TAT Cre


title: ISOGK treated 1


title: covid_p1_1

description: 10x Genomics

value: bronchoalveolar lavage fluid (BALF)

value: when admission to the ICU (t1)


title: HCT116-MeSChetomin500nM-2-12H

city: Gainesville

first: Alberto

last: Riva

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: University of Florida

data_processing:
Reads were mapped to the human transcriptome (GRCh38) with STAR, version 2.5.2b.
Gene expression was quantified using RSEM, version 1.3.3.
Differential gene expression analysis was performed with the edgeR package.
Assembly: GRCh38
Supplementary files format and content: Fold changes, P-values, and normalized counts for every gene in each sample.

growth_protocol: HCT116 cells were seeded in 6-well plates at 2 × 10^5 cells/well in Dulbecco's Modified Eagle Medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (Sigma) and 1% Antibiotic-Antimycotic solution (Gibco), left overnight to attach and acclimate.

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen) according to manufacturer instructions.
Illumina RNA library construction and sequencing were performed at the Interdisciplinary Center for Biotechnology Research (ICBR) Gene Expression Core, University of Florida (UF) ..  For library construction, RNA samples were measured by the QUBIT fluorescent method (Invitrogen) and Agilent Bioanalyzer. An amount of 250 ng of high quality of total RNA with RIN of 7 or higher was used for library construction using the reagents provided in the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, catalog # E7490) and the NEBNext Ultra II Directional RNA Library Prep Kit (New England  Biolabs, catalog #E7760) according to the manufacturer's user guide. Briefly, 200 ng of total RNA was used for mRNA isolated using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, catalog # E7490). Then the poly A enriched RNA was fragmented in NEBNext First Strand Synthesis Buffer via incubation at 94 °C for the desired time. This step was followed by first-strand cDNA synthesis using reverse transcriptase and random hexamer primer.  Synthesis of ds cDNA is done using the 2nd strand master mix provided in the kit, followed by end-repair and dA-tailing.  At this point, Illumina adaptors are ligated to the sample.  Finally, library was amplified, and followed by purification with AMPure beads (Beckman Coulter, catalog # A63881).  The library size and mass were assessed by analysis in the Agilent TapeStation using a High Sensitivity DNA1000 Screen Tape.  Typically, a 250-900 library peak is observed with the highest peak at ~420 bp. Barcoded libraries were pooled equimolarly for sequencing simultaneously for NavaSeq 6000 S4 2x150 cycles run as described below aiming for 50 million reads per sample. RNA-seq library performed at UF ICBR Gene Expression Core (https://biotech.ufl.edu/gene-expression-genotyping/, RRID:SCR_019145).   For Illumina NovaSeq6000 sequencing, Normalized libraries were submitted to the “Free Adapter Blocking Reagent” protocol (FAB, Cat# 20024145) in order to minimize the presence of adaptor-dimers and index hopping rates.  The library pool was diluted to 0.8 nM and sequenced on one S4 flow cell lane (2x150 cycles) of the Illumina NovaSeq6000. The instrument’s computer utilized the NovaSeq Control Software v1.6. Cluster and SBS consumables were v1.5. The final loading concentration of the library was 120 pM with 1% PhiX spike-in control. One lane generated 2.5-3 billion paired-end reads (~950Gb) with an average Q30%>= 92.5% and Cluster PF= 85.4%. FastQ files were generated using the BCL2fastQ function in the Illumina BaseSpace portal. The Illumina NovaSeq 6000 was used to sequence the libraries for 2 x 150 cycles. Sequencing was performed at the ICBR NextGen Sequencing (https://biotech.ufl.edu/next-gen-dna/, RRID:SCR_019152).

treatment_protocol: Cells were treated with solvent control (DMSO, 0.5%), chaetocin, chetomin or their respective sulfide-depleted analogs  to final concentration of 500 nM for 5 H or 12 H.

value: colorectal carcinoma

tag: replicate

value: biol rep 2

value: MeS-Chetomin, 500 nM


title: ISOGK treated 2

value: Liver

value: Apoe-/-

value: ISOGK


title: Normal_2

value: Blood plasma

value: WT


title: HCT116-MeSChaetocin500nM-2-12H

value: MeS-Chaetocin, 500 nM


title: Vehicle control 3

value: vehicle


title: HCT116-Chetomin500nM-2-12H

value: Chetomin, 500 nM


title: HDAC3_Osr2OE_rep2

city: Xiamen

first: Dawang

last: Zhou

state: Fujian

address: Xiang'an south rd, Xiang'an district

department: Life Science

institute: Xiamen University

data_processing:
Raw sequencing reads were trimmed and filtered for quality using CutAdapt (v.2.6). Paired-end reads were aligned using Bowtie2 (v.2.3.5.1) (PMID: 22388286) against mm10 genome.
Aligned reads were sorted and non-uniquely mapping reads were marked using Picard (v.2.9.5) (http://broadinstitute.github.io/picard/). PCR duplicates, reads mapped to mitochondria or of low mapping quality were filtered using Samtools (v.1.9) (PMID: 19505943).
To correct for the fact that the Tn5 transposase binds as a dimer and inserts two adapters in the Tn5 tagmentation step, all positive-strand reads were shifted 4 bp downstream and all negative-strand reads were shifted 5 bp upstream to center the reads on the transposon binding event.
We then pooled the shifted reads by sample type and identified peaks using MACS2 (v.2.2.6) (PMID: 18798982) with a threshold of FDR-corrected p < 0.001 using the Benjamini-Hochberg procedure for multiple hypothesis correction. A union peak list for each experiment was created by combining all peaks in all samples; overlapping peaks were merged with minimum overlap > 0.5. The number of reads in each peak was determined with Diffbind (v.3.6.3) (PMID: 22217937).
Differentially expressed peaks were identified after DESeq2 normalization using a FDR cut-off of 0.05. Peaks were annotated using R package ChIPseeker (v.1.18.0) (PMID: 25765347).
Assembly: mm10
Supplementary files format and content: BigWig Track Format of each Cut&Tag sample.
Library strategy: Cut&Tag

source_name: primary CD8 T cell

growth_protocol: CD8+ T cells were enriched from the spleens and peripheral lymph nodes of donor mice using a naïve CD8+ T cell isolation kit. Cells were resuspended at 106 per ml in RPMI1640 complete medium with 10% FBS (Gibco), 50 M β-mercaptoethanol, 100 U ml-1 penicillin-streptomycin, non-essential amino acids (Gibco) and sodium pyruvate (Gibco).

extract_protocol:
1 × 10^5  CD8+ T cells were collected and washed once with 500 μl wash buffer before they were bound to ConA beads for 10 min at 25 °C.
Cells were incubated with 1 mg of respective targeting antibodies at 4 °C overnight. 0.5 mg secondary antibody was added and incubated for 1 h at 25 °C. Then cells were washed three times with DIG wash buffer and incubated with 0.04 μM pA/G–Tnp for 1 h at 25 °C. Similarly, cells were washed three times with DIG 300 buffer, resuspended in tagmentation buffer and incubated at 37 °C for 1 h. Tagmentation was stopped by adding proteinase K, buffer LB and DNA extract beads. To perform sample wise normalization, 1 pg DNA spike-in form E.coli genome were added per 10^6 cells as internal control. After incubation at 55 °C for 10 min, cells were plated on a magnet and unbound liquid was removed. Beads were gently rinsed twice with 80% ethanol and DNA was eluted with double-distilled water. libraries were barcoded using TruePrep™ Index Kit V2 for lllumina (Vazyme TD202) and amplified for 14 cycles. Final product was cleaned by VAHTS DNA Clean Beads at a 2 × ratio. Libraries were sequenced on a Novaseq 6000 in a 150 bp/150 bp Paired end run. An average of 20 × 106 paired reads was generated per sample.

treatment_protocol: After 24 hours of activation by anti-CD3/CD28, 3 million activated CD8+ T cells were resuspended in the mix of 1 ml fresh 1640 complete RPMI and 3 ml viral supernatant containing 1g ml-1 anti-CD3 and 1 g ml-1 anti-CD28, 50 U ml-1 IL-2 and Polybrene (YEASEN), transferred to 6-well plates, and spun at 800g, 30°C for 60 min. Retroviral supernatants were produced by transfecting the retroviral packaging cell line Plat-Eco (Cell Biolabs) with a retrovirus expression plasmid using Trans-IT (Mirus). This process was repeated the next day. Transduced T cells were cultured for 6 additional days, replacing media and adding fresh IL-2 (50 U ml-1) every day

value: primary CD8 T cell

value: pMIG-Osr2 transduced

tag: cut-tag antibody

value: anti-HDAC3 (ABclonal Technology, A2139)


title: Vehicle control 4


title: HDAC3_Osr2OE_rep1


title: Normal_1

value: healthy control

value: Isolation and purification from human plasma

value: Small RNA


title: HCT116-Chaetocin500nM-2-12H

value: colorectal carcinoma

value: Chaetocin, 500 nM


title: HDAC3_Vector_rep1

value: pMIG-Vector transduced


title: AIS_5

value: adolescents with idiopathic scoliosis


title: Vehicle control 1

value: Liver

value: Apoe-/-


title: HCT116-DMSO-2-12H

value: biol rep 2

value: vehicle control (0.5%DMSO)


title: H3K27AC_Osr2OE_rep2

value: WT

value: anti-H3K27ac (Cell Signaling Technology, 8173S)


title: HCT116-MeSChetomin500nM-2-5H

value: MeS-Chetomin, 500 nM


title: AIS_4

value: Blood plasma


title: MOLM14_DOX_2

data_processing:
Adaptor sequences were trimmed from the raw RNA-seq reads with fastp (v 0.23.1). Trimmed reads of each sample were mapped to the reference human genome hg38 and mouse genome mm10 by using STAR (v 2.3.1) and normalized to 1 million reads in the original library.
The quality of paired reads were checked using FASTQC (v0.11.7)
Reads were aligned against human mm10 genome using HISAT2 (v2.0.5)
Each gene-level raw counts were calculated using featureCounts (v1.5.2)
Assembly: hg38 and mm10
Supplementary files format and content: The CSV file include raw read counts for each sample

growth_protocol: The cells were cultured in RPMI1640 medium with 10% fetal bovine serum FBS and 1% penicillin and streptomycin . 10ng/mL of human IL-3 was added to the medium for culturing TF-1. MLL-AF9-expressing cells were cultured with IMDM) with 10% FCS, 10 ng/mL of SCF, 10 ng/mL of IL-3, and 10 ng/mL of IL-6.

extract_protocol:
RNA was extracted using RNeasy Plus Mini Kit (Qiagen) following manufacturer's protocol
RNA libraries were prepared according to the protocol of QuantSeq 3'mRNA-Seq Library Prep Kit FWD (Lexogen).

treatment_protocol: To induce knockdown of TRAF6 in human cells, the cells were cultured with doxycycline (1μg/mL) for 7 days. For knockout of Traf6 in murine AML cells, the leukemic cells were cultured with 1μM 4-hydroxytamoxifen for 4 days.

value: leukemic cells

value: TRAF6 knockdown

value: Doxycycline


title: H3K27AC_Vector_rep2

value: primary CD8 T cell


title: AIS_2

value: Isolation and purification from human plasma

value: Small RNA


title: HCT116-Chetomin500nM-2-5H

value: colorectal carcinoma

value: Chetomin, 500 nM


title: MOLM14_DOX_3


title: H3K27AC_Osr2OE_rep1

value: pMIG-Osr2 transduced


title: AIS_3

value: adolescents with idiopathic scoliosis


title: KO_2cell_B

first: Zongliang

last: Jiang

department: Animal Sciences

data_processing:
Acquired reads were trimmed using Trim Galore v0.4.1
Trimmed reads were mapped onto the mouse reference genome assembly GRCm38 using Hisat2 v2.0.5.
RNA expression was quantified as fragments per kilobase per million (FPKM) values in Seqmonk v1.40.0
The genes were considered differentially expressed if they provided a false discovery rate of <0.05 and fold change >2.
Gene Ontology (GO) and KEGG pathways were analyzed in R.
Assembly: GRCm38
Supplementary files format and content: txt
Supplementary files format and content: raw counts

source_name: Embryo

extract_protocol:
cDNA libraries were prepared using SMART-seq v4 ultra low input RNA kit (Takara Bio).
The RNA sequencing was performed by NovaSeq v4 (Illumina) with 150 bp read length, paired-end.

treatment_protocol: 6-10 week old BL6 females (CPEB3 HET and CPEB3 KO ) were superovulated by intraperitoneal injection of 5 IU of pregnant mare serum gonadotropin (PMSG). GV oocytes were obtained from dissected ovaries 46 h after stimulation.  To obtain MII oocytes in vivo, 5 IU hCG (ProSpec) was administered 48 h post PMSG. Zygotes were obtained from PMSG-primed females mated with males 17 h post hCG and cultured in vitro in M16 medium under paraffin oil (Ovoil, Vitrolife). 2cell embryos were collected 37 h post hCG administration.

value: Embryo

value: 2-cell embryo

value: KO


title: HCT116-MeSChetomin500nM-1-12H

value: biol rep 1


title: HCT116-MeSChaetocin500nM-2-5H

value: biol rep 2

value: MeS-Chaetocin, 500 nM


title: Th0 IgG

city: Turku

first: Riitta

last: Lahesmaa

address: Tykistökatu 6A

department: Turku Bioscience

country: Finland

institute: University of Turku

data_processing:
Read quality-check and adapter trimming was performed using FastQC (v.0.11.4) (17) and TrimGalore (v. 0.4.5) (https://www.bioinformatics.babraham.ac. uk/projects/trim_galore/), respectively.
The trimmed reads were mapped to the hg38 reference genome using Bowtie2 (v. 2.3.3.1) (23).
Peaks were identified and quantified using the peak caller MACS2 (v. 2.1.0) (24). MACS2 quantifies the peak signal by calculating a fold enrichment value for the peak summit. against random Poisson distribution with local lambda, which is a dynamic parameter defined for each candidate peak. Local lambda captures the influence of local biases and is robust against occasional low read counts at small local regions.
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

source_name: blood

growth_protocol: Ficoll (GE Healthcare, cat# 17-1440-03) was used to isolate PBMCs from human umbilical cord blood samples from Turku University Central Hospital, which was followed by CD4+ T cells were isolation (Invitrogen (cat# 11331D).

extract_protocol: CUT&Tag

treatment_protocol: CD4+ T cells were activated using a plate coated anti-CD3 antibody (Beckman Coulter, cat# IM-1304), and anti-CD28 antibody (Beckman Coulter, cat# IM1376) was added in X-vivo 20 serum-free medium (Lonza, Bazel, Switzerland) containing 0.5 million cells/mL complemented with L-glutamine (2 mM, Sigma-Aldrich) and antibiotics (50 U/mL penicillin and 50 μg/mL streptomycin; Sigma-Aldrich) was used for the cultures. Cells were plated at a density of 2 million cells per well and cultured at 37° C in 5% CO2.

value: blood

tag: antibody

value: IgG

value: CD4+ T cells

value: Activated by CD3/CD28 in absence of cytokines for 72 h


title: HDAC3_Vector_rep2

value: primary CD8 T cell

value: WT

value: pMIG-Vector transduced

value: anti-HDAC3 (ABclonal Technology, A2139)


title: AIS_6

value: Blood plasma

value: Isolation and purification from human plasma

value: Small RNA


title: HCT116-MeSChaetocin500nM-1-12H

value: colorectal carcinoma


title: MOLM14_DOX_1

value: leukemic cells

value: TRAF6 knockdown

value: Doxycycline


title: Normal_6

value: healthy control


title: H3K27AC_Vector_rep1

value: anti-H3K27ac (Cell Signaling Technology, 8173S)


title: Vehicle control 2

value: Liver

value: Apoe-/-

value: vehicle


title: AIS_1

value: adolescents with idiopathic scoliosis


title: HCT116-Chaetocin500nM-2-5H

value: biol rep 2

value: Chaetocin, 500 nM


title: KO_2cell_D

value: Embryo

value: 2-cell embryo

value: KO


title: HCT116-Chetomin500nM-1-12H

value: biol rep 1

value: Chetomin, 500 nM


title: MOLM14_untreated_3

value: Control

value: Untreated


title: HCT116-DMSO-2-5H

value: colorectal carcinoma

value: vehicle control (0.5%DMSO)


title: TF-1_DOX_2

value: leukemic cells

value: TRAF6 knockdown

value: Doxycycline


title: Het_2cell_E

value: Het


title: MOLM14_untreated_2


title: MOLM14_untreated_1


title: iTreg H3K4me3

value: blood

value: CD4+ T cells

value: Activated under iTreg condition for 72 h


title: TF-1_DOX_3


title: TF-1_untreated_3


title: KO_2cell_A


title: iTreg IgG

value: IgG


title: Het_2cell_B

value: Embryo


title: KO_2cell_C

value: 2-cell embryo


title: HCT116-MeSChetomin500nM-1-5H

value: MeS-Chetomin, 500 nM


title: Het_2cell_D


title: Th0 H3K4me3

value: Activated by CD3/CD28 in absence of cytokines for 72 h


title: Het_2cell_C


title: HAP1 WT #7

type: RNA

city: Bethesda

first: Stefan

last: Muljo

state: MD

address: 10 Center Drive

institute: NIH, NIAID

data_processing:
Processed RCC files were imported into nSolver Analysis Software v4.0.70. All samples passed the default nSolver QC checks for Imaging, Binding Density, Positive Control Linearity and Positive Control Limit of Detection.
Background Subtraction and Thresholding steps were skipped and raw gene expression counts were normalized using the geometric means of the Positive Controls (POS_A, POS_B, POS_C, POS_D, POS_E, POS_F) and Housekeeping genes (ABCF1, ALAS1, GUSB, HPRT1, MRPS7, NMT1, OAZ1, PGK1, SDHA, and TBP). Two housekeeping genes, NRDE2 and STK11IP, were excluded from the normalization due to low average counts (<100).
All samples fell within the default Threshold Min and Threshold Max values for Positive Control Normalization (Min 0.3, Max 3.0) and CodeSet Content Normalization (Min 0.1, Max 10.0).
Ratio Data analysis was performed with default parameters to compute fold change estimates, t-test P values and 95% confidence intervals between the MATR3KO and WT samples.
Normalized counts, fold changes and P values were imported into RStudio v1.4.1717 (running R v4.1.1) to generate gene expression heatmaps (R package: pheatmap) and volcano plots (R package: ggplot2).

label: Nanostring

source_name: HAP1 cell line

growth_protocol: HAP1 cells were cultured in IMDM medium (Quality Biological, cat# 112-035-101) supplemented with 10% (vol/vol) heat-inactivated fetal calf serum (Gibco, cat# 26170-043), 100 U/mL penicillin, 100 µg/mL streptomycin (Gibco, cat# 15140-122), at 37° C in a humidified incubator containing 5% CO2.

extract_protocol: HAP1 WT and MATR3 KO cells were lysed by RNAzol (Sigma, cat#R4533-100ML??) to prepare total RNA for sequencing using the DirectZol RNA miniPrep Plus (ZYMO RESEARCH, CAT#R2072) per manufacturer’s instruction.

treatment_protocol: MATR3 KO clones 1 and 5 were purchased from Horizon Discovery (cat# HZGHC007500c001, and HZGHC007500c005) alongside Wild Type controls (cat# C631_29281, batch 40661 ~ Clone #1, and cat# C631_29281, batch 50047 ~ Clone #7)

value: Wild Type


title: MATR3 KO #1

value: MATR3 knockout


title: HCT116-DMSO-1-12H

value: biol rep 1


title: HCT116-Chetomin500nM-1-5H

value: colorectal carcinoma

value: Chetomin, 500 nM


title: TF-1_untreated_2

value: leukemic cells

value: Control

value: Untreated


title: HCT116-Chaetocin500nM-1-12H

value: Chaetocin, 500 nM


title: HCT116-MeSChaetocin500nM-1-5H

value: MeS-Chaetocin, 500 nM


title: MATR3 KO #5


title: PFA_Retina_rep4

city: Philadelphia

first: Raghavi

last: Sudharsan

address: 3900 Delancey Street

institute: University of Pennsylvania

data_processing:
The fastq files were pseudo-aligned to the canine reference transcriptome (ROS_Cfam_1.0) and transcripts per million (TPM) was calculated using kallisto version 0.48.0.
The quantification data were summarized to genes employing the tximport package and normalized using the trimmed mean of M values (TMM) method in edgeR in R.
Genes with <1 count per million (CPM) across all groups were filtered out.
The normalized filtered data underwent variance stabilization through the voom function in the limma package in R.
Differentially expressed genes (³2-fold and £5% false discovery rate) were identified with linear modeling using limma after correcting for multiple testing using Benjamini-Hochberg.
Assembly: ROS_Cfam_1.0
Supplementary files format and content: Tab-delimited text file includes log2 CPM values for each sample.

organism: Canis lupus familiaris

source_name: Retina

extract_protocol:
Total RNA was extracted from FF and PFA-fixed samples using the RNeasy Plus Micro kit and the RNeasy FFPE kit, respectively.
For the PFA-fixed samples, specific modifications were made to the manufacturer’s protocol. The solubilized tissue sections were incubated with Proteinase K for 18 hours at 56°C for improved RNA extraction efficiency, and a second round of genomic DNA digestion was performed using the DNA-free™ DNA Removal kit post RNA extraction to ensure complete removal of genomic DNA contamination.
Sequencing libraries were constructed from RNA extracted from 4 FF and 4 PFA-fixed tissue samples using the SMARTer Stranded Total RNA-Seq kit v3 - Pico Input Mammalian.

treatment_protocol:
The left eyes were fixed in 4% PFA in 0.1 M PBS for 3 hours, followed by an additional 24-hour fixation in 2% PFA in 0.1 M PBS at 4°C. Subsequently, the eyecup was dissected into four quadrants, and the tissues were cryoprotected sequentially for 24 hours each in 15% and 30% sucrose solutions in 0.1 M PBS at 4°C. After cryopreservation, the PFA-fixed tissues were also embedded in optimal cutting medium (OCT) medium, following rapid freezing.
For the right eye, the eyecup was dissected into four quadrants and the tissue sections embedded in OCT medium without fixation and cryoprotection.

value: Retina

tag: background breed

value: Beagle

value: 31 weeks

tag: Sex

value: Male

value: wild-type

value: PFA-fixed, frozen


title: THP-1_DOX_3

value: TRAF6 knockdown

value: Doxycycline


title: KO_MII_E

source_name: Oocyte

value: Oocyte

value: MII oocyte

value: KO


title: HAP1 WT #1

value: Wild Type


title: KO_MII_D


title: TF-1_untreated_1

value: leukemic cells


title: TF-1_DOX_1


title: Het_2cell_A

value: Embryo

value: 2-cell embryo

value: Het


title: PFA_Retina_rep3


title: THP-1_untreated_3

value: Control

value: Untreated


title: HCT116-Chaetocin500nM-1-5H

value: colorectal carcinoma

value: biol rep 1

value: Chaetocin, 500 nM


title: PFA_Retina_rep2

value: Retina

value: Beagle

value: 31 weeks

value: Male

value: wild-type


title: Donor2, WT, CART19

first: Puneeth

last: Guruprasad

state: Pennsylvania

address: 3400 Civic Center Blvd

data_processing:
RNA libraries were sequenced on an Illumina NovaSeq6000 using paired-end sequencing
Sequences were mapped to the GRCh38 reference genome
Differentially expressed genes between WT or BTLA KO anti-CD19 CAR T cells were calculated using DESeq2
Assembly: GRCh38
Supplementary files format and content: csv file includes RPKM values for each Sample

source_name: T cells

growth_protocol: OCI-Ly18 cell line and human CAR T cells were grown and cultured in standard culture media “R10” (RPMI 1640 + 10% FBS, 1% Penicillin/Streptomycin, 1% HEPES, 1% GlutaMAX) at 37°C in 5% ambient CO2 and maintained at a concentration of 1 × 106 cells/mL

extract_protocol:
On day 15, RNA from WT or BTLA KO CAR T cells was harvested and purified using Rneasy mini plus kit (Qiagen). > 1 microgram of RNA was used for library construction
Libraries were constructed at NovoGene Coporation Inc and sequenced using their services.

tag: individual

value: T cells

value: WT

value: Repeated stimulation with cancer cells (OCI-Ly18)

value: Day 15


title: FF_Retina_rep3

value: Fresh frozen


title: Donor1, BTLA KO, CART19

value: BTLA KO


title: Het_MII_E

value: Oocyte

value: MII oocyte

value: Het


title: FF_Retina_rep2


title: KO_MII_C

value: KO


title: T2DM rep4

city: Leeds

first: Jim

middle: R

last: Boyne

address: Leeds Beckett University

department: Biomedical Science

country: United Kingdom

institute: Leeds Beckett University

description: small RNA

data_processing:
Raw reads were subjected to adaptor trimming using Cutadapt v2.5 and aligned to the GRCh38/hg38 assembly of the human genome using Bowtie2 v2.3.5.1.
HTSeq-count v0.11.1 was used to quantify the miRNA abundance based on the human miRNA annotation (miRBase Release 22.1) with parameters (-s no -a 10 -m union --nonunique none).
Assembly: GRCh38
Supplementary files format and content: Comma-delimited text file includes raw counts for each sample

source_name: Venous Blood Platelets

extract_protocol:
Human blood was taken by venepuncture into acid citrate dextrose buffer and platelet-rich plasma (PRP) obtained by centrifugation of whole blood at 200g at 20°C, 20 minutes. Washed platelets were isolated from the PRP by centrifugation at 800g at 20°C, 12 min in the presence of prostaglandin E1 (PGE1; 50 ng/ml) and platelets were resuspended in Tyrodes buffer. PMV release was induced with thrombin (0.1 U/ml) for 60 min and stopped by EDTA (20 mM). PMVs were isolated by centrifugation at 20,000g for 90 minutes at 18°C, then resuspended in Tyrodes buffer.
Total RNA was extracted from PMVs using the Aurum total RNA Mini kit (BIO-RAD, UK) according to the manufacturer's instructions.
Small RNA-Seq libraries were prepared using NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB, UK).

value: Venous Blood Platelets

value: Platelet microvesicles

tag: diagnosis

value: type 2 diabetes (T2DM)

value: Thrombin induction of PMV release


title: THP-1_DOX_1

value: leukemic cells

value: TRAF6 knockdown

value: Doxycycline


title: Donor2, BTLA KO, CART19

value: T cells


title: PFA_Retina_rep1

tag: tissue

value: Retina

value: Beagle

value: 31 weeks

value: Male

value: wild-type

value: PFA-fixed, frozen


title: KO_MII_B

value: Oocyte

value: MII oocyte


title: IgG_LNA2_replicate2

value: blood

value: IgG

value: CD4+ T cells

value: LIRIL2R LNA2

value: Nucleofected with NT LNAs followed by resting for 24 hours followed by activation under Treg condition for 48 h


title: FF_Retina_rep4

value: Fresh frozen


title: THP-1_untreated_2

tag: cell line

value: leukemic cells

value: Control

value: Untreated


title: KO_MII_A

tag: cell type

value: KO


title: IgG_LNA2_replicate1

tag: genotype


title: Het_MII_B

value: Het


title: iPSC-NPC-Xenograft-PCTME biol rep 3

city: Chicago

first: Xiao

last: Song

state: IL

address: 303 E Superior St, Lurie 6-250

department: Neurology

institute: Northwestern University Feinberg School of Medicine

data_processing:
Reads were aligned to the human genome hg19 using HISAT2, version 2.1.0.
For xenograft samples, the Disambiguate tool (AstraZeneca-NGS) was used to separate sequence reads originating from human iPSC cells and mouse stomal component after alignment. The reads assigned to human species were used for gene expression and alternative splicling analysis.
Quantification was performed using HTSeq-count, version 0.13.5.
The counts for a gene in each sample was normalized by DESeq2, version 1.34.0.
The mapped reads were processed through the MISO (version 0.5.4) pipeline to estimate expression of alternatively spliced isoforms.
Assembly: hg19
Supplementary files format and content: HTSeq-count files include raw counts for each gene of each sample generated from HTSeq-count.
Supplementary files format and content: MISO files include Percent Spliced In (PSI) values for each AS events of each sample generated from MISO-run and MISO-summary.
Supplementary files format and content: Normalized_counts files include the normalized counts for each gene in all samples generated from DESeq2.

organism: Homo sapiens/Mus musculus xenograft

source_name: brain with xenograft

growth_protocol: iPSC-NPCs were cultured in N2B27 medium (50% DMEM/F12 and 50% Neurobasal-A medium supplemented with GlutaMAX, 1 × N-2 supplement, 1 × B-27 supplement, 1 × antibiotic-antimycotic, 150 µM ascorbic acid) plus 3 μM CHIR99021 and 1 μM SAG. Organoids were cultured in N2B27 medium plus 10% FBS.

extract_protocol:
RNA was isolated using the Qiagen RNeasy Mini kit according to the manufacturer's instruction. 1 ug of total RNA was used for the construction of sequencing libraries.
Libraries were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module, Ultra II RNA Library Prep Kit, and Multiplex Oligos (NEB, Cat #E7490, E7775, E6609) according to the manufacturer's instruction.

treatment_protocol: For organoid samples, edited NPCs were cultured in 3D organoid with N2B27+10%FBS medium for 14 days. For xenograft samples, NPCs with different genotypes were intracranially transplanted into athymic mice. Mice were sacrificed when pathologic symptoms developed resulting from tumor burden or 120 days post brain transplantation. RNAs were extracted from the tumor region of brain tissue sections and subjected to RNA-seq analysis.

value: brain with xenograft

value: Edited human iPSC12-derived NPCs

value: PTEN-/-, CDKN2A/B-/-, TERTp-C228T/WT, MTAP-/-, EGFRvIII

tag: treatment

value: implanted into mouse brain


title: Donor1, WT, CART19

value: T cells

value: WT

value: Repeated stimulation with cancer cells (OCI-Ly18)

tag: time

value: Day 15


title: Het_MII_D

value: Oocyte

value: MII oocyte


title: THP-1_untreated_1


title: THP-1_DOX_2

value: TRAF6 knockdown

value: Doxycycline


title: HCT116-DMSO-1-5H

value: colorectal carcinoma

value: biol rep 1

value: vehicle control (0.5%DMSO)


title: T2DM rep1

description: small RNA

value: Venous Blood Platelets

value: Platelet microvesicles

value: type 2 diabetes (T2DM)

value: Thrombin induction of PMV release


title: iPSC-NPC-Xenograft-PCTME biol rep 1

value: brain with xenograft

value: Edited human iPSC12-derived NPCs

value: PTEN-/-, CDKN2A/B-/-, TERTp-C228T/WT, MTAP-/-, EGFRvIII


title: T2DM rep2

description: small RNA


title: Het_MII_C

value: Het


title: iPSC-NPC-Xenograft-PCTME biol rep 2

value: implanted into mouse brain


title: old fasted/refed

city: New York

first: Paul

middle: Vincent

last: Dellorusso

state: NY

address: 701 West 168th Street, 724 Hammer Health Sciences Center

department: Genetics and Development

institute: Columbia University Irving Medical Center

data_processing:
QC was performed keeping cells with more than 500 genes detected, less than 100,000 total reads, and less than 20% mitochondrial reads.
Downstream analyses were done using Scanpy with cells normalized to 10,000 UMIs per cell and logarithmically transformed.
Highly variable genes (HVGs) were selected using the “FindVariableFeatures” method”. UMAP visualizations were obtained from 50 PCA components.
Cell clusters were defined using either Louvain or Leiden algorithms.
Assembly: mm10
Supplementary files format and content: CSV files containing differential gene expression by cluster
Supplementary files format and content: CSV files containing differential pathway analysis by cluster

source_name: bone marrow

extract_protocol:
~ 30,000 HSCs were sorted into 1.5 ml tubes containing 500 µl of HBSS/2% FBS and transferred to the Columbia Genome Center Single Cell Analysis Core Facility for microfluidic cell processing, library preparation and sequencing.
~10,000 HSCs were loaded for each sample and 1 sample was loaded per condition.

value: bone marrow

value: purified hematopoietic stem cells

value: hematopoietic stem cell

value: Old

value: 24hr fast/24hr refeed


title: H3K27ac_LNA2_replicate2

value: blood

value: CD4+ T cells

value: LIRIL2R LNA2

value: Nucleofected with NT LNAs followed by resting for 24 hours followed by activation under Treg condition for 48 h


title: iPSC-NPC-Xenograft-PCTE biol rep 3

value: PTEN-/-, CDKN2A/B-/-, TERTp-C228T/WT, EGFRvIII


title: FF_Retina_rep1

value: Retina

value: Beagle

value: 31 weeks

value: Male

value: wild-type

value: Fresh frozen


title: Control rep6 (C10)

description: small RNA

value: Venous Blood Platelets

value: Platelet microvesicles

value: non-diabetic

value: Thrombin induction of PMV release


title: H3K27ac_LNA2_replicate1


title: IgG_LNA1_replicate2

value: IgG

value: LIRIL2R LNA1


title: iPSC-NPC-Xenograft-PCTE biol rep 2

value: brain with xenograft

value: Edited human iPSC12-derived NPCs

value: implanted into mouse brain


title: old fasted

value: bone marrow

value: purified hematopoietic stem cells

value: hematopoietic stem cell

value: Old

value: 24 hr fast


title: Control rep5 (C9)

description: small RNA


title: Control rep4 (C8)

description: small RNA


title: IgG_LNA1_replicate1

value: blood

value: CD4+ T cells

value: Nucleofected with NT LNAs followed by resting for 24 hours followed by activation under Treg condition for 48 h


title: H3K27ac_LNA1_replicate2


title: iPSC-NPC-Xenograft-PCTE biol rep 1

value: PTEN-/-, CDKN2A/B-/-, TERTp-C228T/WT, EGFRvIII


title: young fasted/refed

value: Young

value: 24hr fast/24hr refeed


title: Control rep3 (C6)

description: small RNA

value: Venous Blood Platelets

value: Platelet microvesicles

value: non-diabetic

value: Thrombin induction of PMV release


title: Het_MII_A

value: Oocyte

value: MII oocyte

value: Het


title: iPSC-NPC-Xenograft-TIA biol rep 2

value: brain with xenograft

value: Edited human iPSC12-derived NPCs

value: implanted into mouse brain


title: H3K27ac_LNA1_replicate1

value: LIRIL2R LNA1


title: T2DM rep3

description: small RNA

value: type 2 diabetes (T2DM)


title: young fasted

value: bone marrow

value: purified hematopoietic stem cells

value: hematopoietic stem cell

value: 24 hr fast


title: Control rep2 (C2)

description: small RNA


title: iPSC-NPC-Xenograft-TIA biol rep 3


title: IgG_NT_replicate2

value: blood

value: IgG

value: CD4+ T cells

value: NT LNA

value: Nucleofected with NT LNAs followed by resting for 24 hours followed by activation under Treg condition for 48 h


title: young ad libidum

value: Young

value: ad lib


title: IgG_NT_replicate1


title: old 2

data_processing:
For 10X, QC was performed keeping cells with more than 500 genes detected, less than 100,000 total reads, and less than 20% mitochondrial reads. Downstream analyses were done using Scanpy with cells normalized to 10,000 UMIs per cell and logarithmically transformed. Highly variable genes (HVGs) were selected using the “FindVariableFeatures” method”. UMAP visualizations were obtained from 50 PCA components. Cell clusters were defined using either Louvain or Leiden algorithms.
For SmartSeq2, reads were mapped to the Mus musculus genome (EMSEMBL GRCm38.p4 Release 81) and ERCC sequences using GSNAP (version 2015-09-29) with parameters: -A sam –B 5 –t 24 –n 1 –Q –N 1. HTseq-count56 was used to count reads mapped to each gene, with parameters: –s no. All cells with < 100,000 reads mapping to endogenous RNA and >20% reads mapping to mitochondrial genes were considered low quality and removed from downstream analyses. Data were normalized and highly variable genes were identified as previously described57, using a false discovery rate threshold equal to 0.1 for the chi-squared test.
Assembly: EMSEMBL GRCm38.p4 Release 81
Supplementary files format and content: CSV files containing differential gene expression by cluster are provided.

extract_protocol:
For 10X Genomics sequencing, ~ 30,000 HSCs were sorted into 1.5 ml tubes containing 500 µl of HBSS/2% FBS and transferred to the Columbia Genome Center Single Cell Analysis Core Facility for microfluidic cell processing, library preparation and sequencing. For SmartSeq2 sequencing, Single yHSC, AThi oHSC, ATmid oHSC, and ATlo oHSC were directly sorted into individual wells of a 96-well PCR plate in 2.3 µl of lysis buffer containing 0.2% Triton X-100 (Sigma-Aldrich) and 1U of Superase-In RNase Inhibitor (Ambion). Cells were frozen immediately at -80°C until further processing.
For 10X, ~10,000 HSCs were loaded for each sample and 1 sample was loaded per condition.  For SmartSeq2, after thawing on ice, 2 µl of an annealing mixture containing1 µM oligodT (IDT), 5 mM each dNTPs and a 1:6,000,000 dilution of ERCC RNA Spike-In Mix (Invitrogen) was added followed by incubation at 72°C for 3 min. Then 5.7 µl of a Reverse Transcription mix containing 3.5 U/µl of Maxima H minus retrotranscriptase (ThermoFisher), 0.88 U/µl of Superase-In RNase Inhibitor, 1.75x Maxima RT Buffer, 3.5 µM TSO (Qiagen) and 13.15% PEG 8000 (Sigma-Aldrich) was added and the mixture was incubated at 42°C for 90 min, followed by 70°C for 15 min. cDNA was further amplified by adding 40 µl of a PCR mix containing 0.03 U/µl of Terra PCR direct polymerase (Takara Bio), 1.25x Terra PCR Direct Buffer, and 0.25 µM IS PCR primer (ID). PCR was as follows: 3 min at 98°C for initial denaturation followed by 21 cycles of 15 s at 98°C, 30 s at 65°C, 4 min at 68°C. Final elongation was performed for 10 min at 72°C. Following preamplification, all samples were purified using Ampure XP beads (Beckman Coulter) at a ratio of 1:0.6 with a final elution in 25 µl of EB Buffer (Qiagen). The cDNA was then quantified using the Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher). Size distributions were checked on high-sensitivity DNA chips (Agilent Bioanalyzer).
For 10X, samples were sequenced using an Illumina HiSEQ 4000 instrument. For SmartSeq2, samples were used to construct Nextera XT libraries (Illumina) from 100 pg of preamplified cDNA. Libraries were purified and size selected (0.5x-0.7x) using Ampure XP beads. Libraries were quantified using KAPA qPCR quantification kit (KAPA Biosystems), pooled and sequenced using an Illumina HiSEQ 4000 instrument.

value: purified hematopoietic stem cell

value: Old

value: steady state isolation


title: iPSC-NPC-Xenograft-TIA biol rep 1

value: brain with xenograft

value: Edited human iPSC12-derived NPCs

value: implanted into mouse brain


title: iPSC-NPC-Xenograft-TI biol rep 3


title: old 1

value: bone marrow


title: iPSC-NPC-Xenograft-TI biol rep 2


title: bud3

city: Vancouver

first: Howard

last: Cen

state: BC

address: 2350 Health Sciences Mall

country: Canada

institute: University of British Columbia

data_processing:
Sequencing was performed on Illumina NextSeq500 sequencer with 42 bp x 42 bp paired-end reads and completed at BRC Sequencing Core facility at the University of British Columbia.
Sequencing data were de-multiplexed using Illumina's bcl2fastq2 and the de-multiplexed reads were then aligned to the Homo sapiens (UCSC hg19) reference genome using STAR (Aligner) software (STAR_2.5.0b version).
Assembly was done using Cufflinks software (2.2.1 version) with default settings on the Illumina Sequence Hub.
Assembly: hg19
Supplementary files format and content: Tab-delimited .txt file containing raw counts of all the samples.

source_name: HUES4 PDXeG

extract_protocol:
Total RNA from isolated buds and bodies (n = 4 independent batches of differentiation) was extracted and frozen in QIAzol, and then purified together using QIAzol reagent according to the manufacturer’s protocol.
Quality control (QC) test of RNA samples was performed using Agilent 2100 Bioanalyzer (Agilent). Samples passing the QC test (RIN > 8.0) were then library prepared following the standard protocol for NEBNext Ultra II Stranded mRNA (New England Biolabs).

value: HUES4 PDXeG

value: Differentiated hPSC

value: Intact buds of stage 6 spheroids


title: H3K27ac_NT_replicate2

value: blood


title: old ad libidum

value: purified hematopoietic stem cells

value: hematopoietic stem cell


title: H3K27ac_NT_replicate1

value: CD4+ T cells

value: NT LNA


title: bud2


title: bud1


title: young 1

value: Young


title: iPSC-NPC-Xenograft-TI biol rep 1


title: young 2


title: Control rep1 (C1)

description: small RNA

value: Venous Blood Platelets

value: Platelet microvesicles

value: non-diabetic

value: Thrombin induction of PMV release


title: body4

value: Intact bodies of stage 6 spheroids


title: LIRIL2R_oddProbes_rep2

data_processing:
Read quality-check and adapter trimming was performed using FastQC (v.0.11.4) (17) and TrimGalore (v. 0.4.5) (https://www.bioinformatics.babraham.ac. uk/projects/trim_galore/), respectively.
The trimmed reads were mapped to the hg38 reference genome using Bowtie2 (v. 2.3.3.1) (23).
Peaks were identified and quantified using the peak caller MACS2 (v. 2.1.0) (24). MACS2 quantifies the peak signal by calculating a fold enrichment value for the peak summit. against random Poisson distribution with local lambda, which is a dynamic parameter defined for each candidate peak. Local lambda captures the influence of local biases and is robust against occasional low read counts at small local regions.
Assembly: hg38
Supplementary files format and content: bigwig and narrow peak

source_name: Blood

extract_protocol:
A total of 19 Chromatin Isolations via RNA Precipitation (ChIRP) probes tiling LIRIL2R were designed at BIOSEARCH TECHNOLOGIES. The probes were serially numbered, based on their position across the transcript. Even and odd probes were then pooled to ensure specificity of the pull-down. The published ChIRP protocol was used for the RNA pull down (Chu et al. 2012) following the instructions of the kit (EZ-Magna ChIRP RNA Interactome Kit, Cat# 17-10495, Merck Millipore).
A modified ChIP-seq protocol and illumina ChIP-seq TrueSeq kit were used for preparing the libraries, which were sequenced (2x100bp; 40 million reads/library) on an illumina NovaSeq 6000 instrument.

value: Blood

value: unmodified

value: Activated under iTreg conditions for 48 hours


title: LIRIL2R_input_rep2


title: IgG_rep2

data_processing:
Raw sequencing reads were trimmed and filtered for quality using CutAdapt (v.2.6). Paired-end reads were aligned using Bowtie2 (v.2.3.5.1) (PMID: 22388286) against mm10 genome.
Aligned reads were sorted and non-uniquely mapping reads were marked using Picard (v.2.9.5) (http://broadinstitute.github.io/picard/). PCR duplicates, reads mapped to mitochondria or of low mapping quality were filtered using Samtools (v.1.9) (PMID: 19505943).
To correct for the fact that the Tn5 transposase binds as a dimer and inserts two adapters in the Tn5 tagmentation step, all positive-strand reads were shifted 4 bp downstream and all negative-strand reads were shifted 5 bp upstream to center the reads on the transposon binding event.
We then pooled the shifted reads by sample type and identified peaks using MACS2 (v.2.2.6) (PMID: 18798982) with a threshold of FDR-corrected p < 0.001 using the Benjamini-Hochberg procedure for multiple hypothesis correction. A union peak list for each experiment was created by combining all peaks in all samples; overlapping peaks were merged with minimum overlap > 0.5. The number of reads in each peak was determined with Diffbind (v.3.6.3) (PMID: 22217937).
Differentially expressed peaks were identified after DESeq2 normalization using a FDR cut-off of 0.05. Peaks were annotated using R package ChIPseeker (v.1.18.0) (PMID: 25765347).
Assembly: mm10
Supplementary files format and content: BigWig Track Format of each sample.

extract_protocol:
1 × 10^5  CD8+ T cells were collected and washed once with 500 μl wash buffer before they were bound to ConA beads for 10 min at 25 °C.
Cells were incubated with 1 mg of respective targeting antibodies at 4 °C overnight. 0.5 mg secondary antibody was added and incubated for 1 h at 25 °C. Then cells were washed three times with DIG wash buffer and incubated with 0.04 μM pA/G–Tnp for 1 h at 25 °C. Similarly, cells were washed three times with DIG 300 buffer, resuspended in tagmentation buffer and incubated at 37 °C for 1 h. Tagmentation was stopped by adding proteinase K, buffer LB and DNA extract beads. After incubation at 55 °C for 10 min, cells were plated on a magnet and unbound liquid was removed. Beads were gently rinsed twice with 80% ethanol and DNA was eluted with double-distilled water. libraries were barcoded using TruePrep™ Index Kit V2 for lllumina (Vazyme TD202) and amplified for 14 cycles. Final product was cleaned by VAHTS DNA Clean Beads at a 2 × ratio. Libraries were sequenced on a Novaseq 6000 in a 150 bp/150 bp Paired end run. An average of 20 × 106 paired reads was generated per sample.

value: primary CD8 T cell

value: WT

value: pMIG-Osr2 transduced

value: Normal mouse IgG(Abcam, ab188776)


title: body3

value: HUES4 PDXeG

value: Differentiated hPSC


title: Arabidopsis, lon1_2atg5_3, rep3

city: Tianjin

first: Ce

address: Weijin road NO.94

institute: Nankai University

data_processing:
The transcriptome sequencing and analysis were conducted by OE biotech Co., Ltd. (Shanghai, China).
Raw data (raw reads) were processed using Trimmomatic.
The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
Then the clean reads were mapped to reference genome using hisat2
Assembly: TAIR10.1
Supplementary files format and content: FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Supplementary files format and content: DEGs were identified using the DESeq(2012) R package functions estimateSizeFactors and nbinomTest. Pvalue < 0.05 and foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential expression.

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Arabidopsis grown best under 16/8 hours light / dark cycle at room temperature (18-22 ° C), with light intensity of 120-150 µ mol / m2 (normal conditions).

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis
The libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Then these libraries were sequenced on the Illumina sequencing platform (DNBSEQ-T7) and 125bp/150bp paired-end reads were generated.

treatment_protocol: treat under normal conditions

value: seedling

value: double mutant

value: normal conditions


title: Arabidopsis, lon1_2atg5_2, rep2


title: LIRIL2R_evenProbes_rep1

value: CD4+ T cells


title: Arabidopsis, lon1_2atg5_1, rep1


title: IgG_rep1

value: pMIG-Vector transduced

value: Normal Rabbit IgG(Cell Signaling Technology, 2729)


title: body2


title: Flag-Osr2_Osr2OE_rep3

source_name: primary CD9 T cell

value: primary CD9 T cell

value: anti-DYKDDDDK (Santa Cruz, sc166355)


title: Arabidopsis, atg5_1_3, rep3

value: ATG5 knockout


title: LIRIL2R_oddProbes_rep1

value: Blood

value: unmodified


title: body1

value: Intact bodies of stage 6 spheroids


title: Flag-Osr2_Osr2OE_rep2

value: primary CD8 T cell

value: WT

value: anti-DYKDDDDK (Cell Signaling Technology, 14793)


title: LIRIL2R_input_rep1

value: Activated under iTreg conditions for 48 hours


title: Normal_5

city: Los Angeles

first: Ana

middle: C

last: Maretti-Mira

address: 1450 Biggy Street, NRT 3514

department: Medicine

institute: USC

data_processing:
The raw sequencing reads were first checked for overall quality and adapter contamination using FastQC and trimmed using TrimGalore prior to downstream analysis.
Reads were then mapped to the GENCODE version 35 human genome reference using the STAR aligner.
Significantly differentially expressed genes were identified using the Bioconductor package DESeq2 with a model that accounted for the effects of sex (i.e. ~ sex + group) and a significance threshold of an adjusted p-value of < 0.1.
Assembly: GENCODE version 35 human
Supplementary files format and content: individual tab-delimited text files include raw counts for the samples included in this study

source_name: Peripheral blood

extract_protocol:
Blood was collected in Vacutainer EDTA tubes (BD Biosciences). Human neutrophils were isolated using MACSxpress® Whole Blood Neutrophil Isolation Kit, human (Miltenyi Biotech) following the manufacturer’s protocol. Purity of isolated neutrophils was assessed using flow cytometry (CD15+CD16+CD14-CD193-). Greater than 90% purity was achieved for all samples.
RNA was isolated using RNeasy Mini kit (Qiagen) and RNA integrity was analyzed by 2100 Expert Bioanalyzer System (Agilent), using the Agilent RNA 6000 Pico Kit (Agilent).
Libraries were simultaneously prepared from extracted total RNA using Illumina Truseq Stranded mRNA library preparation kit according to the manufacturer’s protocol (Illumina).
Prepared libraries were sequenced on the Illumina Nextseq500 at 30 million reads per sample at 2x75 cycles.

value: Peripheral blood

value: Neutrophil

tag: disease state

value: healthy


title: LIRIL2R_evenProbes_rep2


title: bud4

value: HUES4 PDXeG

value: Differentiated hPSC

value: Intact buds of stage 6 spheroids


title: Normal_4


title: Flag-Osr2_Osr2OE_rep1

value: pMIG-Osr2 transduced


title: Arabidopsis, atg5_1_1, rep1

value: seedling

value: normal conditions


title: 18_LNA2_rep3_72h_S18_LANE2

data_processing:
Read quality-check and adapter trimming was performed using FastQC (v.0.11.4) (17) and TrimGalore (v. 0.4.5) (https://www.bioinformatics.babraham.ac. uk/projects/trim_galore/), respectively.
The trimmed reads were mapped to the hg38 reference genome using Bowtie2 (v. 2.3.3.1) (23).
Open chromatin regions were identified and quantified using the peak caller MACS2 (v. 2.1.0) (24). MACS2 quantifies the peak signal by calculating a fold enrichment value for the peak summit. against random Poisson distribution with local lambda, which is a dynamic parameter defined for each candidate peak. Local lambda captures the influence of local biases and is robust against occasional low read counts at small local regions.
The regions were annotated using HOMER (v.4.9)
Assembly: hg38
Supplementary files format and content: bigwig and narrow peak

growth_protocol: Ficoll (GE Healthcare, cat# 17-1440-03) was used to isolate PBMCs from human umbilical cord blood samples from Turku University Central Hospital, which was followed by CD4+ T cells were isolation (Invitrogen (cat# 11331D).  CD4+ T cells were activated using a plate coated anti-CD3 antibody (Beckman Coulter, cat# IM-1304), and anti-CD28 antibody (Beckman Coulter, cat# IM1376) was added in X-vivo 20 serum-free medium (Lonza, Bazel, Switzerland) containing 0.5 million cells/mL complemented with L-glutamine (2 mM, Sigma-Aldrich) and antibiotics (50 U/mL penicillin and 50 μg/mL streptomycin; Sigma-Aldrich) was used for the cultures. Cells were plated at a density of 2 million cells per well and cultured at 37° C in 5% CO2.

extract_protocol:
Nuclei were isolated, and the libraries were prepared using Nextera DNA library preparation kit with i7 and i5 indices (15028212). AMPURE-XP beads (B46053, Beckman Coulter) were used to purify the libraries.
All samples were pooled into one pool and sequenced on two lanes.

treatment_protocol: For LNA transfections, 4 million cells mixed with 150 pmols of LNA, prepared in 100 μL volume of OptiMEM (Gibco by Life Technologies, cat # 31985-047), were used to transfect the cells using the Amaxa Nucleofector II system (Lonza). After transfection, cells were first rested at 37° C for 48 h in RPMI 1640 (Sigma-Aldrich) medium supplemented with 10% FCS, 50 U/mL penicillin, 50 μg/mL streptomycin, and 2 mM L-glutamine and then activated and cultured as described above

value: blood

value: CD4+ T cells

value: LIRIL2R LNA2

value: Activated under iTreg condition for 72 hours


title: 18_LNA2_rep3_72h_S18_LANE1


title: Normal_3


title: Normal_2


title: 17_LNA1_rep3_72h_S17_LANE1

value: LIRIL2R LNA1


title: Normal_1

value: MASH


title: 604-CNTNAP2-KO-AD-M_S17_L002

city: Povo (TN)

first: ENRICO

last: DOMENICI

address: via Sommarive n. 9

department: CELLULAR, COMPUTATIONAL AND INTEGRATIVE BIOLOGY

country: Italy

institute: University of Trento

description:
604-CNTNAP2
S17

data_processing:
Trimming - Alignment and feature count
Trimming with Trim_galore
Alignment with STAR
Feature count with STAR
Assembly: GRCm39.primary_assembly.genome.fa.gz
Supplementary files format and content: Matrix of gene counts

organism: Mus

source_name: cerebella

extract_protocol:
Brain samples used for flow cytometry were homogenized with pestles immediately after dissections and single-cell suspension were generated using Falcon 70 um cell strainer (Corning). After the isolation, brain cells were washed with complete medium and incubated for 12h at 37°C. Total RNAs were extracted from cerebral cerebella of adult Cntnap2 +/+  Cntnap2-/- mice using RNeasy Plus Mini Kit (Qiagen), and retro-transcribed to cDNA according to published protocol.
The quality and the integrity of the RNA samples, RNA Integrity Numbers (RIN) were assessed using a 2100 Bioanalyzer Instrument (Agilent). Only samples with RIN > 8 were considered for the analysis. Libraries were prepared using a TruSeq Stranded mRNA Library Prep (48 Samples) Kit (Illumina). Library preparation, quality check, and sequencing were carried out using Illumina NovaSeq6000.

value: cerebella

value: KO

value: adult (AD)

value: M

tag: groups

value: KO-AD-M


title: 802-CNTNAP2-WT-AD-M_S10_L002

description:
802-CNTNAP2
S10

value: WT

tag: age

value: WT-AD-M


title: 47-CNTNAP2-WT-AD-M_S8_L002

description:
47-CNTNAP2
S8


title: Mild_3

value: Peripheral blood

value: Neutrophil


title: 17_LNA1_rep3_72h_S17_LANE2


title: 503-CNTNAP2-WT-P30-M_S23_L002

description:
503-CNTNAP2
S23

value: Thirty (30) days post-natal (P30)


title: Arabidopsis, atg5_1_2, rep2

value: seedling

value: ATG5 knockout

value: normal conditions


title: 16_NT_rep3_72h_S16_LANE1

value: blood

value: CD4+ T cells

value: NT LNA


title: 544-CNTNAP2-KO-P30-F_S38_L002

description:
544-CNTNAP2
S38

value: F


title: 15_LNA2_rep3_24h_S15_LANE1

value: LIRIL2R LNA2

value: Activated under iTreg condition for 24 hours


title: PAI-039 Treatment Replicate 3

first: Wenwen

last: Zhang

state: Jiangsu

address: 68 Changle Road

institute: Nanjing Medical University

hyb_protocol: Scanned on an Agilent G2565AA scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: PAI-039-treated MDA-MB-231 Cells

label_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

growth_protocol: MDA-MB-231 cells were kept in an undifferentiated, pluripotent state by using 1000 IU/ml leukemia inhibitory factor (LIF; Chemicon, ESGRO, ESG1107), and grown on top of murine embryonic fibroblasts feeder layer inactivated by 10 ug/ml of mitomycin C (Sigma, St. L

extract_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

treatment_protocol: Total RNA extracted using Trizol following manufacturer's instructions

value: MDA-MB-231 cell

value: PAI-039 treatment


title: 15_LNA2_rep3_24h_S15_LANE2


title: Mild_1

value: MASH


title: Advanced_4


title: 966-CNTNAP2-WT-P30-M_S21_L002

description:
966-CNTNAP2
S21

value: cerebella

value: WT

value: M


title: PAI-039 Treatment Replicate 2


title: PAI-039 Treatment Replicate 1


title: PAI-1 Treatment Replicate 2

source_name: PAI-1-treated MDA-MB-231 Cells

value: PAI-1 treatment


title: 501-CNTNAP2-WT-P30-M_S22_L002

description:
501-CNTNAP2
S22

value: Thirty (30) days post-natal (P30)


title: 16_NT_rep3_72h_S16_LANE2

value: Activated under iTreg condition for 72 hours


title: Advanced_3

value: Peripheral blood

value: Neutrophil


title: 545-CNTNAP2-WT-P30-M_S24_L002

description:
545-CNTNAP2
S24


title: Advanced_2


title: PAI-1 Treatment Replicate 1


title: 978-CNTNAP2-WT-AD-M_S6_L002

description:
978-CNTNAP2
S6

value: adult (AD)

value: WT-AD-M


title: Control MDA-MB-231 Replicate 3

source_name: MDA-MB-231 Cells

value: Control


title: PAI-1 Treatment Replicate 3


title: Control MDA-MB-231 Replicate 2


title: 13_NT_rep3_24h_S13_LANE2

source_name: blood

value: blood

value: CD4+ T cells

value: NT LNA


title: Mild_2


title: 14_LNA1_rep3_24h_S14_LANE1

value: LIRIL2R LNA1

value: Activated under iTreg condition for 24 hours


title: PBMC Control

city: Guangzhou

first: Zhenhua

last: Luo

state: Guangzhou

address: Number 58, zhongshan er road, Yuexiu,

institute: The First Affiliated Hospital, Sun Yat-sen University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: coculture with DMEM medium (control) treated human cholangiocyte cell line H69

extract_protocol:
Human peripheral blood mononuclear cells (PBMC) was harvested from peripheral blood. PBMC were cocultured with rotavirus treated or DMEM medium treated human cholangiocyte cell line H69. Then, PBMC was harvested for Single cell RNA sequencing.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

tag: subject

value: healthy donor

value: PBMC


title: 13_NT_rep3_24h_S13_LANE1


title: Advanced_1

value: MASH


title: 890-CNTNAP2-KO-P30-M_S30_L002

description:
890-CNTNAP2
S30

value: cerebella

value: KO

value: M


title: PBMC RRV

description: 10x Genomics

source_name: coculture with rotavirus (RRV) treated human cholangiocyte cell line H69


title: 891-CNTNAP2-KO-P30-F_S35_L002

description:
891-CNTNAP2
S35

value: Thirty (30) days post-natal (P30)

value: F


title: 333-CNTNAP2-KO-AD-M_S19_L002

description:
333-CNTNAP2
S19

value: KO-AD-M


title: 12_LNA2_rep2_72h_S12_LANE2

value: LIRIL2R LNA2

value: Activated under iTreg condition for 72 hours